FluxAnalyzer: A Graphical User Interface for Analyzing Structural Properties and Fluxes in Balanced Metabolic Networks. - Steffen Klamt; Ernst Dieter Gilles (German Conference on Bioinformatics, 2001)

Making predictions about robustness and flexibility from metabolic network structure. - Stefan Schuster; Steffen Klamt; Jörg Stelling (German Conference on Bioinformatics, 2003)

FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. - Steffen Klamt; Jörg Stelling; Martin Ginkel; Ernst Dieter Gilles (Bioinform., 2003)

Minimal cut sets in biochemical reaction networks. - Steffen Klamt; Ernst Dieter Gilles (Bioinform., 2004)

Computation of elementary modes: a unifying framework and the new binary approach. - Julien Gagneur; Steffen Klamt (BMC Bioinform., 2004)

Workbench zur Modellbildung, Simulation und Analyse zellulärer Systeme (Workbench for Model Set Up, Simulation, and Analysis of Cellular Systems). - Andreas Kremling; Steffen Klamt; Martin Ginkel; Ernst Dieter Gilles (it Inf. Technol., 2004)

A methodology for the structural and functional analysis of signaling and regulatory networks. - Steffen Klamt; Julio Saez-Rodriguez; Jonathan A. Lindquist; Luca Simeoni; Ernst Dieter Gilles (BMC Bioinform., 2006)

Visual setup of logical models of signaling and regulatory networks with ProMoT. - Julio Saez-Rodriguez; Sebastian Mirschel; Rebecca Hemenway; Steffen Klamt; Ernst Dieter Gilles; Martin Ginkel (BMC Bioinform., 2006)

Structural and functional analysis of cellular networks with CellNetAnalyzer. - Steffen Klamt; Julio Saez-Rodriguez; Ernst Dieter Gilles (BMC Syst. Biol., 2007)

A Logical Model Provides Insights into T Cell Receptor Signaling. - Julio Saez-Rodriguez; Luca Simeoni; Jonathan A. Lindquist; Rebecca Hemenway; Ursula Bommhardt; Boerge Arndt; Utz-Uwe Haus; Robert Weismantel; Ernst Dieter Gilles; Steffen Klamt; Burkhart Schraven (PLoS Comput. Biol., 2007)

Host-pathogen systems biology: logical modelling of hepatocyte growth factor and Helicobacter pylori induced c-Met signal transduction. - Raimo Franke; Melanie Müller; Nicole Wundrack; Ernst Dieter Gilles; Steffen Klamt; Thilo Kähne; Michael Naumann (BMC Syst. Biol., 2008)

Computing Knock-Out Strategies in Metabolic Networks. - Utz-Uwe Haus; Steffen Klamt; Tamon Stephen (J. Comput. Biol., 2008)

Computing paths and cycles in biological interaction graphs. - Steffen Klamt; Axel von Kamp (BMC Bioinform., 2009)

Transforming Boolean models to continuous models: methodology and application to T-cell receptor signaling. - Dominik M. Wittmann; Jan Krumsiek; Julio Saez-Rodriguez; Douglas A. Lauffenburger; Steffen Klamt; Fabian J. Theis (BMC Syst. Biol., 2009)

Hypergraphs and Cellular Networks. - Steffen Klamt; Utz-Uwe Haus; Fabian J. Theis (PLoS Comput. Biol., 2009)

The Logic of EGFR/ErbB Signaling: Theoretical Properties and Analysis of High-Throughput Data. - Regina Samaga; Julio Saez-Rodriguez; Leonidas G. Alexopoulos; Peter K. Sorger; Steffen Klamt (PLoS Comput. Biol., 2009)

CASOP GS: Computing Intervention Strategies Targeted at Production Improvement in Genome-scale Metabolic Networks. - Katrin Bohl; Luis F. de Figueiredo; Oliver Hädicke; Steffen Klamt; Christian Kost; Stefan Schuster; Christoph Kaleta (GCB, 2010)

TRANSWESD: inferring cellular networks with transitive reduction. - Steffen Klamt; Robert J. Flassig; Kai Sundmacher (Bioinform., 2010)

Computing Combinatorial Intervention Strategies and Failure Modes in Signaling Networks. - Regina Samaga; Axel von Kamp; Steffen Klamt (J. Comput. Biol., 2010)

From Binary to Multivalued to Continuous Models: The Lac Operon as a Case Study. - Raimo Franke; Fabian J. Theis; Steffen Klamt (J. Integr. Bioinform., 2010)

Special issue: Integration of OMICs datasets into Metabolic Pathway Analysis. - Christoph Kaleta; Luis F. de Figueiredo; Ines Heiland; Steffen Klamt; Stefan Schuster (Biosyst., 2011)

An application programming interface for CellNetAnalyzer. - Steffen Klamt; Axel von Kamp (Biosyst., 2011)

Metabolic network modeling of redox balancing and biohydrogen production in purple nonsulfur bacteria. - Oliver Hädicke; Hartmut Grammel; Steffen Klamt (BMC Syst. Biol., 2011)

Minimal cut sets in a metabolic network are elementary modes in a dual network. - Kathrin Ballerstein; Axel von Kamp; Steffen Klamt; Utz-Uwe Haus (Bioinform., 2012)

An effective framework for reconstructing gene regulatory networks from genetical genomics data. - Robert J. Flassig; Sandra Heise; Kai Sundmacher; Steffen Klamt (Bioinform., 2013)

Comparison and improvement of algorithms for computing minimal cut sets. - Christian Jungreuthmayer; Govind Nair; Steffen Klamt; Jürgen Zanghellini (BMC Bioinform., 2013)

SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools. - Claudine Chaouiya; Duncan Bérenguier; Sarah M. Keating; Aurélien Naldi; Martijn P. van Iersel; Nicolas Rodriguez 001; Andreas Dräger; Finja Büchel; Thomas Cokelaer; Bryan M. Kowal; Benjamin Wicks; Emanuel J. V. Gonçalves; et al. (BMC Syst. Biol., 2013)

Reconstruction of large-scale regulatory networks based on perturbation graphs and transitive reduction: improved methods and their evaluation. - Andrea Pinna 003; Sandra Heise; Robert J. Flassig; Alberto de la Fuente; Steffen Klamt (BMC Syst. Biol., 2013)

Detecting and Removing Inconsistencies between Experimental Data and Signaling Network Topologies Using Integer Linear Programming on Interaction Graphs. - Ioannis N. Melas; Regina Samaga; Leonidas G. Alexopoulos; Steffen Klamt (PLoS Comput. Biol., 2013)

Stoichiometric and Constraint-Based Analysis of Biochemical Reaction Networks. - Steffen Klamt; Oliver Hädicke; Axel von Kamp (Large-Scale Networks in Engineering and Life Sciences, 2014)

A model integration approach linking signalling and gene-regulatory logic with kinetic metabolic models. - Anke Ryll; Joachim Bucher; Anne Bonin; Sophia Bongard; Emanuel J. V. Gonçalves; Julio Saez-Rodriguez; Jens Niklas; Steffen Klamt (Biosyst., 2014)

Enumeration of Smallest Intervention Strategies in Genome-Scale Metabolic Networks. - Axel von Kamp; Steffen Klamt (PLoS Comput. Biol., 2014)

Genome-scale strain designs based on regulatory minimal cut sets. - Radhakrishnan Mahadevan; Axel von Kamp; Steffen Klamt (Bioinform., 2015)

Extended notions of sign consistency to relate experimental data to signaling and regulatory network topologies. - Sven Thiele; Luca Cerone; Julio Saez-Rodriguez; Anne Siegel; Carito Guziolowski; Steffen Klamt (BMC Bioinform., 2015)

An algorithm for the reduction of genome-scale metabolic network models to meaningful core models. - Philipp Erdrich; Ralf Steuer; Steffen Klamt (BMC Syst. Biol., 2015)

Disentangling the Complexity of HGF Signaling by Combining Qualitative and Quantitative Modeling. - Lorenza Alice D'Alessandro; Regina Samaga; Tim Maiwald; Seong-Hwan Rho; Sandra Bonefas; Andreas Raue; Nao Iwamoto; Alexandra Kienast; Katharina Waldow; Rene Meyer; Marcel Schilling; Jens Timmer; et al. (PLoS Comput. Biol., 2015)

Exact quantification of cellular robustness in genome-scale metabolic networks. - Matthias P. Gerstl; Steffen Klamt; Christian Jungreuthmayer; Jürgen Zanghellini (Bioinform., 2016)

TRaCE+: Ensemble inference of gene regulatory networks from transcriptional expression profiles of gene knock-out experiments. - S. M. Minhaz Ud-Dean; Sandra Heise; Steffen Klamt; Rudiyanto Gunawan (BMC Bioinform., 2016)

From elementary flux modes to elementary flux vectors: Metabolic pathway analysis with arbitrary linear flux constraints. - Steffen Klamt; Georg Regensburger; Matthias P. Gerstl; Christian Jungreuthmayer; Stefan Schuster; Radhakrishnan Mahadevan; Jürgen Zanghellini; Stefan Müller 009 (PLoS Comput. Biol., 2017)

OptMDFpathway: Identification of metabolic pathways with maximal thermodynamic driving force and its application for analyzing the endogenous CO2 fixation potential of Escherichia coli. - Oliver Hädicke; Axel von Kamp; Timur Aydogan; Steffen Klamt (PLoS Comput. Biol., 2018)

Generalizing Diffuse Interface Methods on Graphs: Nonsmooth Potentials and Hypergraphs. - Jessica Bosch; Steffen Klamt; Martin Stoll (SIAM J. Appl. Math., 2018)

Characterizing and ranking computed metabolic engineering strategies. - Philipp Schneider; Steffen Klamt (Bioinform., 2019)

RedCom: A strategy for reduced metabolic modeling of complex microbial communities and its application for analyzing experimental datasets from anaerobic digestion. - Sabine Koch; Fabian Kohrs; Patrick Lahmann; Thomas Bissinger; Stefan Wendschuh; Dirk Benndorf; Udo Reichl; Steffen Klamt (PLoS Comput. Biol., 2019)

Designing Optimal Experiments to Discriminate Interaction Graph Models. - Sven Thiele; Sandra Heise; Wiebke Hessenkemper; Hannes Bongartz; Melissa Fensky; Fred Schaper; Steffen Klamt (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Automatic construction of metabolic models with enzyme constraints. - Pavlos Stephanos Bekiaris; Steffen Klamt (BMC Bioinform., 2020)

Speeding up the core algorithm for the dual calculation of minimal cut sets in large metabolic networks. - Steffen Klamt; Radhakrishnan Mahadevan; Axel von Kamp (BMC Bioinform., 2020)

An extended and generalized framework for the calculation of metabolic intervention strategies based on minimal cut sets. - Philipp Schneider; Axel von Kamp; Steffen Klamt (PLoS Comput. Biol., 2020)

Designing microbial communities to maximize the thermodynamic driving force for the production of chemicals. - Pavlos Stephanos Bekiaris; Steffen Klamt (PLoS Comput. Biol., 2021)

CNApy: a CellNetAnalyzer GUI in Python for analyzing and designing metabolic networks. - Sven Thiele; Axel von Kamp; Pavlos Stephanos Bekiaris; Philipp Schneider; Steffen Klamt (Bioinform., 2022)

StrainDesign: a comprehensive Python package for computational design of metabolic networks. - Philipp Schneider; Pavlos Stephanos Bekiaris; Axel von Kamp; Steffen Klamt (Bioinform., 2022)

Towards a modeling, optimization and predictive control framework for fed-batch metabolic cybergenetics. - Sebastián Espinel-Ríos; Bruno Morabito; Johannes Pohlodek; Katja Bettenbrock; Steffen Klamt; Rolf Findeisen (CoRR, 2023)

Balancing biomass reaction stoichiometry and measured fluxes in flux balance analysis. - Axel von Kamp; Steffen Klamt (Bioinform., 2023)

Minimal cut sets in metabolic networks: from conceptual foundations to applications in metabolic engineering and biomedicine. - Steffen Klamt; Jürgen Zanghellini; Axel von Kamp (Briefings Bioinform., 2024)

Experimentally implemented dynamic optogenetic optimization of ATPase expression using knowledge-based and Gaussian-process-supported models. - Sebastián Espinel-Ríos; Gerrich Behrendt; Jasmin Bauer; Bruno Morabito; Johannes Pohlodek; Andrea Schütze; Rolf Findeisen; Katja Bettenbrock; Steffen Klamt (CoRR, 2024)